New Tool to Map RNA-DNA Interactions Could Help Researchers Translate Gene Sequences into Functions

Bioengineers at the University of California (UC) San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that is capable of providing a full account of all the RNA molecules that interact with a segment of DNA, as well as the locations of all these interactions -- in just a single experiment. RNA molecules can attach to particular DNA sequences to help control how much protein these particular genes produce within a given time, and within a given cell. And by knowing what genes produce these regulatory RNAs, researchers can start to identify new functions and instructions encoded in the genome. "Most of the human genome sequence is now known, but we still don't know what most of these sequences mean," said Dr. Sheng Zhong, bioengineering professor at the UC San Diego Jacobs School of Engineering and the study's lead author. "To better understand the functions of the genome, it would be useful to have the entire catalog of all the RNA molecules that interact with DNA, and what sequences they interact with. We've developed a tool that can give us that information." Dr. Zhong and his team published their findings in the February 20, 2017 issue of Current Biology. The article is titled “Systematic Mapping of RNA-Chromatin Interactions in Vivo.” Existing methods to study RNA-DNA interactions are only capable of analyzing one RNA molecule at a time, making it impossible to analyze an entire set of RNA-DNA interactions involving hundreds of RNA molecules. "It could take years to analyze all these interactions," said Tri Nguyen, a bioengineering Ph.D. student at UC San Diego and a co-first author of the study.
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